Sodium in PDB 6t53: Thrombin in Complex with A D-Phe-Pro-P-Benzylamine Derivative

All present enzymatic activity of Thrombin in Complex with A D-Phe-Pro-P-Benzylamine Derivative:
3.4.21.5;

The structure of Thrombin in Complex with A D-Phe-Pro-P-Benzylamine Derivative, PDB code: 6t53 was solved by K.Ngo, N.Abazi, A.Heine, G.Klebe, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	38.41 / 1.35
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	70.167, 71.412, 72.475, 90.00, 100.57, 90.00
R / Rfree (%)	12.9 / 15.1

The binding sites of Sodium atom in the Thrombin in Complex with A D-Phe-Pro-P-Benzylamine Derivative (pdb code 6t53). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Thrombin in Complex with A D-Phe-Pro-P-Benzylamine Derivative, PDB code: 6t53:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in the Thrombin in Complex with A D-Phe-Pro-P-Benzylamine Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Thrombin in Complex with A D-Phe-Pro-P-Benzylamine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na301 b:13.2 occ:1.00 O H:HOH475 2.4 15.6 1.0 O H:PHE204A 2.4 10.8 1.0 C H:PHE204A 3.5 11.0 1.0 HA H:PHE204A 3.5 12.8 1.0 CA H:PHE204A 4.1 10.7 1.0 HA H:ASN204B 4.2 15.3 1.0 O H:PRO204 4.5 11.2 1.0 HD21 H:ASN205 4.6 38.4 1.0 N H:ASN204B 4.6 12.0 1.0 HB3 H:PHE204A 4.7 14.4 1.0 HD22 H:ASN205 4.9 38.4 1.0 CA H:ASN204B 4.9 12.7 1.0 ND2 H:ASN205 5.0 32.0 1.0 CB H:PHE204A 5.0 12.0 1.0

Sodium binding site 2 out of 2 in the Thrombin in Complex with A D-Phe-Pro-P-Benzylamine Derivative


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Thrombin in Complex with A D-Phe-Pro-P-Benzylamine Derivative within 5.0Å range: probe atom residue distance (Å) B Occ H:Na302 b:15.9 occ:1.00 O H:ARG221A 2.3 16.1 1.0 O H:LYS224 2.4 14.2 1.0 O H:HOH578 2.4 15.7 0.5 O H:HOH487 2.4 17.2 1.0 O H:HOH485 2.4 13.9 1.0 O H:HOH511 2.6 16.4 1.0 H H:LYS224 3.3 17.4 1.0 C H:ARG221A 3.4 16.5 1.0 C H:LYS224 3.5 12.8 1.0 HA H:ASP222 3.7 21.5 1.0 HA H:ASP221 3.7 18.4 1.0 O H:HOH537 3.8 27.1 1.0 H H:GLY223 3.8 19.1 1.0 N H:LYS224 3.9 14.5 1.0 O H:HOH456 3.9 20.4 1.0 HB2 H:LYS224 4.0 17.6 1.0 O H:TYR184A 4.0 14.1 1.0 N H:ARG221A 4.0 15.8 1.0 O H:HOH578 4.0 14.0 0.5 H H:ARG221A 4.1 19.0 1.0 C H:ASP221 4.1 16.0 1.0 N H:GLY223 4.2 15.9 1.0 HA H:TYR225 4.2 12.9 1.0 N H:ASP222 4.2 17.9 1.0 O H:HOH499 4.2 14.3 1.0 CA H:LYS224 4.2 14.0 1.0 CA H:ASP222 4.3 17.9 1.0 CA H:ARG221A 4.3 16.3 1.0 CA H:ASP221 4.4 15.4 1.0 C H:ASP222 4.5 16.5 1.0 O H:ASP221 4.5 17.2 1.0 N H:TYR225 4.6 11.5 1.0 CB H:LYS224 4.6 14.7 1.0 OD1 H:ASP221 4.6 16.5 1.0 C H:GLY223 4.8 14.2 1.0 CA H:TYR225 4.9 10.7 1.0 HB2 H:ARG221A 4.9 21.7 1.0 HA3 H:GLY184 4.9 13.0 1.0 H H:ASP222 5.0 21.5 1.0

K.Ngo, N.Abazi, A.Heine, G.Klebe. Thrombin in Complex with A D-Phe-Pro-P-Benzylamine Derivative To Be Published.